Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations - PubMed (original) (raw)

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

Björn M Hallström et al. BMC Evol Biol. 2008.

Abstract

Background: A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method.

Results: The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95-100 million years ago. Many of the following divergences occurred only a few (2-4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses.

Conclusion: The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data.

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Figures

Figure 1

Figure 1

Distance distribution of the human-platypus aa sequence alignment.

Figure 2

Figure 2

ML tree on NT12 analysis and ML bootstrap support values (nt/aa) for branches that do not receive maximum support.

Figure 3

Figure 3

Partial trees illustrating the alternative topologies that were statistically evaluated to determine the phylogenetic position of the tree shrew (1–3), the relationships within Rodentia (4–6), the position of the bat (7–11), and the Xenarthra, Afrotheria and Boreoplacentalia relationships (12–14).

Figure 4

Figure 4

Chronogram showing the estimated divergence times. The figure is based on divergence times estimated from nt sequences using TF. Divergences are labeled with letters (a-t) and the exact dates and the values estimated by other methods and sequence data are shown in Table 3.

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References

    1. Cannarozzi G, Schneider A, Gonnet G. A phylogenomic study of human, dog, and mouse. PLoS Comput Biol. 2007;3:1e2. doi: 10.1371/journal.pcbi.0030002. - DOI - PMC - PubMed
    1. Hallström BM, Kullberg M, Nilsson MA, Janke A. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol Biol Evol. 2007;24:2059–2068. doi: 10.1093/molbev/msm136. - DOI - PubMed
    1. Nikolaev S, Montoya-Burgos JI, Margulies EH, Program NCS, Rougemont J, Nyffeler B, Antonarakis S. Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data. PloS Genet. 2007;3:1. doi: 10.1371/journal.pgen.0030002. - DOI - PMC - PubMed
    1. Wildman DE, Uddin M, Opazo JC, Liu G, Lefort V, Guindon S, Gascuel O, Grossman LI, Romero R, Goodman M. Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci USA. 2007;104:14395–14400. doi: 10.1073/pnas.0704342104. - DOI - PMC - PubMed
    1. Novacek MJ. Mammalian phylogeny: shaking the tree. Nature. 1992;356:121–125. doi: 10.1038/356121a0. - DOI - PubMed

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